besmarts.mechanics.molecular_models module

besmarts.mechanics.molecular_models

class besmarts.mechanics.molecular_models.chemical_model(symbol, name, topo)

Bases: object

besmarts.mechanics.molecular_models.chemical_model_iter_smarts_hierarchies(cm: chemical_model)

besmarts.mechanics.molecular_models.chemical_model_iter_smarts_hierarchies_nodes(cm)

class besmarts.mechanics.molecular_models.chemical_model_procedure(name, topo)

Bases: object

assign(pm: physical_model) → physical_model

get_term_labels(key) → Dict

get_term_values(key) → Dict

class besmarts.mechanics.molecular_models.chemical_model_procedure_smarts_assignment(pcp_model: perception_model, topology_terms)

Bases: chemical_model_procedure

assign(cm, pm: physical_model, overrides=None) → physical_model

this will return, for each selection, the reference

get_term_labels(k)

get_term_values(k)

besmarts.mechanics.molecular_models.chemical_model_smarts_hierarchy_add_node(cm, cid, pid, uid, parentid, node_ref, smarts, vals)

besmarts.mechanics.molecular_models.chemical_model_smarts_hierarchy_copy_node(cm: chemical_model, pid, uid, parent, name)

besmarts.mechanics.molecular_models.chemical_model_smarts_hierarchy_remove_node(cm: chemical_model, cid, pid, uid, node)

class besmarts.mechanics.molecular_models.chemical_system(pcp_model: perception_model, models: List[chemical_model])

Bases: object

besmarts.mechanics.molecular_models.chemical_system_get_angle_means(csys, psystems, names=None) → dict

besmarts.mechanics.molecular_models.chemical_system_get_angles(csys, psystems, names=None) → dict

besmarts.mechanics.molecular_models.chemical_system_get_bond_length_means(csys, psystems, names=None) → dict

besmarts.mechanics.molecular_models.chemical_system_get_bond_lengths(csys, psystems, names=None) → dict

besmarts.mechanics.molecular_models.chemical_system_get_ic_measure(csys, psystems, m, fn, names=None) → dict

besmarts.mechanics.molecular_models.chemical_system_get_ic_measure_means(csys, m, kv) → dict

besmarts.mechanics.molecular_models.chemical_system_get_node_hierarchy(csys, node)

besmarts.mechanics.molecular_models.chemical_system_get_node_model(csys, node)

besmarts.mechanics.molecular_models.chemical_system_get_smarts_node(csys, S)

besmarts.mechanics.molecular_models.chemical_system_get_value(csys, key, missing=None)

besmarts.mechanics.molecular_models.chemical_system_get_value_list(csys, key)

besmarts.mechanics.molecular_models.chemical_system_groupby_names(csys, m, psystems, selections, names=None) → dict

from chemical_model m, group the assn by the labels in physical_model m

besmarts.mechanics.molecular_models.chemical_system_iter_keys(csys)

besmarts.mechanics.molecular_models.chemical_system_iter_smarts_hierarchies(csys)

besmarts.mechanics.molecular_models.chemical_system_iter_smarts_hierarchies_nodes(csys)

besmarts.mechanics.molecular_models.chemical_system_print(csys, show_parameters=None)

besmarts.mechanics.molecular_models.chemical_system_reset_angles(csys, psystems, names=None, skip=None) → dict

besmarts.mechanics.molecular_models.chemical_system_reset_bond_lengths(csys, psystems, names=None, skip=None) → dict

besmarts.mechanics.molecular_models.chemical_system_set_value(csys, key, value)

besmarts.mechanics.molecular_models.chemical_system_set_value_list(csys, key, values)

besmarts.mechanics.molecular_models.chemical_system_smarts_complexity(csys: chemical_system, B=1.0, C=1.0)

get all smarts and calculate the smarts complexity

besmarts.mechanics.molecular_models.chemical_system_smarts_hierarchy_add_node(csys, cid, pid, uid, node_ref, smarts, vals: Dict[str, List])

besmarts.mechanics.molecular_models.chemical_system_smarts_hierarchy_get_node_keys(cm, cid, pid, uid, node)

besmarts.mechanics.molecular_models.chemical_system_to_physical_system(cs, pos: List[graph_assignment], ref=None, reuse=None) → physical_model

class besmarts.mechanics.molecular_models.forcefield(models: Dict[str, chemical_model], pcp_model)

Bases: object

metadata: forcefield_metadata

models: Dict[str, chemical_model]

perception: perception_model

class besmarts.mechanics.molecular_models.forcefield_metadata

Bases: object

class besmarts.mechanics.molecular_models.physical_model(positions, labels, values)

Bases: object

The functional form that can be evaluated as a function of positions. Also tracks the positions as a cache mechanism to avoid recomputing Sort of assumes energies/forces are a function of internal coordinates and masses and positions are cartesian

labels: List[Dict]

positions: List[graph_assignment_float]

topology

values: List[Dict]

class besmarts.mechanics.molecular_models.physical_model_procedure(name, topo)

Bases: object

calculates one or more physical properties of a system returns a bunch tables

assign(pm: physical_model)

this will return the compute function and config (i.e. the task) the task will return a assignments.graph_topology_db_table

get_term_labels(key) → Dict

get_term_values(key) → Dict

besmarts.mechanics.molecular_models.physical_model_values_copy(pm)

class besmarts.mechanics.molecular_models.physical_system(models: List[physical_model])

Bases: object

besmarts.mechanics.molecular_models.physical_system_iter_keys(psys_list: physical_system, csys: chemical_system)

Generate a flat mapping of keys and values of only the parameters that were applied to the physical systems

besmarts.mechanics.molecular_models.physical_system_set_value(psys: physical_system, key, value)

besmarts.mechanics.molecular_models.smiles_assignment_function(fn, sys_params, top_params, pos)

besmarts.mechanics.molecular_models.smiles_assignment_matrix_function(fn, sys_params, top_params, posmat)

class besmarts.mechanics.molecular_models.system_term(name, symbol, unit, cast, values, comment='')

Bases: object

class besmarts.mechanics.molecular_models.topology_term(symbol, name, unit, cast, values, comment, value_comments)

Bases: object

copy()

besmarts.mechanics.molecular_models.topology_term_copy(t: topology_term)